Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,108,716	C→T	intergenic (+202/‑118)	pfkA → / → sbp	6‑phosphofructokinase 1/sulfate/thiosulfate ABC transporter periplasmic binding protein Sbp

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,108,716	0	C	T	92.0%	72.8 / ‑0.5	25	intergenic (+202/‑118)	pfkA/sbp	6‑phosphofructokinase 1/sulfate/thiosulfate ABC transporter periplasmic binding protein Sbp
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (13/10);  total (14/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.67e-01

GGTGACTGGCTGGACTGCGCGAAAAAACTGTATTAATGATTTCGGAAAAAGGCAGATTCCTTTACCCTGAAACCGATGACAGAAGCAAAAATGCCTGATGCGCTTCGCTTATCAGGCCTACATGAATTCTGCAATTTATTGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCCTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACGTTTCATATGATCCAACGCGCGAATTGTACGAACAGTACAAC  >  NC_000913/4108479‑4108953                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                              ggTGACTGGCTGGACTGCGCGAAAAAACTGTAGTAATGATTTCGGAAAAAGGCAGATTCCTTTACCCTGAAACCGATGACAGAAGCAAAAATGCCTGATGCGCTTCGCTTATCAGGCCTACATGAATTCTGCAATTTATTGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTGTGAATCCCTc                                                                                                                                                                                                                                  <  2:251058/251‑1 (MQ=255)        ggctggACTGCGCGAAAAAACTGTATTAATGATTTCGGAAAAAGGCAGATTCCTTTACCCTGAAACCGATGACAGAAGCAAAAATGCCTGATGCGCTTCGCTTATCAGGCCTACATGAATTCTGCAATTTATTGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACata                                                                                                                                                                                                                            <  1:149050/250‑1 (MQ=255)                     gAAAAAACTGTATTAATGATTTCGGAAAAAGGCAGATTCCTTTACCCTGAAACCGATGACAGAAGCAAAAATGCCTGATGCGCTTCGCTTATCAGGCCTACATGAATTCTGCAATTTATTGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTtat                                                                                                                                                                                                              >  2:172390/1‑251 (MQ=255)                                 ttAATGATTTCGGAAAAAGGCAGATTCCTTTACCCTGAAACCGATGACAGAAGCAAAAATGCCTGATGCGCTTCGCTTATCAGGCCTACATGAATTCTGCAATTTATTGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCtttt                                                                                                                                                                                                  >  1:89863/1‑251 (MQ=255)                                                                                                tGATGCGCTTCGCTTATCAGGCCTACATGAATTCTGCAATTTATTGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGCCAAAGCGCACTTTGAAAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAag                                                                                                                                     >  1:41124/1‑249 (MQ=255)                                                                                                              tATCAGGCCTACATGAATTCTGCAATTTATTGACTTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGa                                                                                                                      >  2:144644/1‑250 (MQ=255)                                                                                                               aTCAGGCTTACATGAATTCTGCAATTTATTGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGaa                                                                                                                     <  2:282432/250‑1 (MQ=255)                                                                                                                    gCCTACATGAATTCTGCAATTTATTGAATTTGCAACCTTTTGTAGGCCGAATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGCGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCCCGCTTTCCTCATCACAACACAACCTAAGAGAGTCGGGCGATGAACAAggg                                                                                                               >  2:181214/1‑249 (MQ=255)                                                                                                                        aCATGAATTCTGCAATTTATTGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCCTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGc                                                                                                           >  2:67180/1‑251 (MQ=255)                                                                                                                                            tGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTCATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCt                                                                                       >  2:89/1‑251 (MQ=255)                                                                                                                                             gAATTTGCAAACTGTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTACAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGGGGGGCGTAGGGTTAACATTTTTGCt                                                                                       <  2:76773/250‑1 (MQ=255)                                                                                                                                                             gTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGtt                                                                       <  2:226356/250‑1 (MQ=255)                                                                                                                                                               aGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATg                                                                    >  1:270225/1‑251 (MQ=255)                                                                                                                                                                 gCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGCAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGc                                                                  >  2:76353/1‑251 (MQ=255)                                                                                                                                                                     gATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAg                                                              <  1:172390/251‑1 (MQ=255)                                                                                                                                                                                    ccgcATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGcttctt                                               >  1:184680/1‑251 (MQ=255)                                                                                                                                                                                        aTCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACg                                           >  2:148231/1‑251 (MQ=255)                                                                                                                                                                                          ccGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACGt                                          <  2:163788/250‑1 (MQ=255)                                                                                                                                                                                          ccGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCCTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACGtt                                         <  1:67180/251‑1 (MQ=255)                                                                                                                                                                                               aTGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACGTTTCat                                     >  1:74835/1‑250 (MQ=255)                                                                                                                                                                                                 ggACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACGTTTCatat                                   <  2:184680/250‑1 (MQ=255)                                                                                                                                                                                                         cgcACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACGTTTCATATGATCCAAcg                          >  1:58916/1‑251 (MQ=255)                                                                                                                                                                                                           cACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACGTTTCATATGATCCAAcgcg                        <  1:90950/251‑1 (MQ=255)                                                                                                                                                                                                                      cAATATGAGGCGGATTTCTTCCGCTTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACGTTTCATATGATCCAACGCGCGAATTGTACg             >  1:276970/1‑251 (MQ=255)                                                                                                                                                                                                                                 ggATTTCATCCGGTTTTTTAATCCCACAACATATGCCCGCAATGTATAGACAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCGCAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCTTAGGGTTAACTTTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTTAGCTTCTTAACGTTTCATATGATCCAACGCGCGATTTGTACggagaatacaac  <  2:267949/251‑12 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                              GGTGACTGGCTGGACTGCGCGAAAAAACTGTATTAATGATTTCGGAAAAAGGCAGATTCCTTTACCCTGAAACCGATGACAGAAGCAAAAATGCCTGATGCGCTTCGCTTATCAGGCCTACATGAATTCTGCAATTTATTGAATTTGCAAACTTTTGTAGGCCGGATAAGGCGTTCGCGCCGCATCCGGCATGGACAAAGCGCACTTTGTCAGCAATATGAGGCGGATTTCTTCCGCCTTTTTAATCCCTCAACATATACCCGCAAGTTATAGCCAATCTTTTTTTATTCTTTAATGTTTGGTTAACCTTCTGGCACGCTTTGCTCATCACAACACAACATAAGAGAGTCGGGCGATGAACAAGTGGGGCGTAGGGTTAACATTTTTGCTGGCGGCAACCAGCGTTATGGCAAAGGATATTCAGCTTCTTAACGTTTCATATGATCCAACGCGCGAATTGTACGAACAGTACAAC  >  NC_000913/4108479‑4108953

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑